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Reference SNP (refSNP) Cluster Report: rs1053362                 ** With untested allele **
RefSNP
Organism:human (Homo sapiens)
Molecule Type:Genomic
Created/Updated in build:86/151
Map to Genome Build:108/Weight 1
Validation Status:byClusterbyFreqWith1000GenomeData
Citation:PubMedLitVarNEW
Allele
Variation Class:SNV:
single nucleotide variation
RefSNP Alleles:A/C/T (FWD)
Allele Origin:
Ancestral Allele:C
Variation Viewer:link to VariationViewer
Clinical Significance:With untested allele [ClinVar]
MAF/MinorAlleleCount:T=0.0012/128 (ExAC)
T=0.0036/18 (1000 Genomes)
T=0.0030/35 (GO-ESP)
T=0.0036/450 (TOPMED)
HGVS Names
  • CM000663.2:g.25301629C>A
  • CM000663.2:g.25301629C>T
  • NC_000001.10:g.25628120C>T
  • NC_000001.11:g.25301629C>A
  • NC_000001.11:g.25301629C>T
  • NG_007494.1:g.34140C>A
  • NG_007494.1:g.34140C>T
  • NM_001127691.2:c.744C>A
  • NM_001127691.2:c.744C>T
  • NM_001282867.1:c.246C>A
  • NM_001282867.1:c.246C>T
  • NM_001282868.1:c.744C>A
  • NM_001282868.1:c.744C>T
  • NM_001282869.1:c.744C>A
  • NM_001282869.1:c.744C>T
  • NM_001282870.1:c.744C>A
  • NM_001282870.1:c.744C>T
  • NM_001282871.1:c.744C>A
  • NM_001282871.1:c.744C>T
  • NM_001282872.1:c.744C>A
  • NM_001282872.1:c.744C>T
  • NM_001321772.1:c.-67+35411G>A
  • NM_001321772.1:c.-67+35411G>T
  • NM_016124.4:c.744C>A
  • NM_016124.4:c.744C>T
  • NP_001121163.1:p.Ser248=
  • NP_001121163.1:p.Ser248Arg
  • NP_001269796.1:p.Ser82=
  • NP_001269796.1:p.Ser82Arg
  • NP_001269797.1:p.Ser248=
  • NP_001269797.1:p.Ser248Arg
  • NP_001269798.1:p.Ser248=
  • NP_001269798.1:p.Ser248Arg
  • NP_001269799.1:p.Ser248=
  • NP_001269799.1:p.Ser248Arg
  • NP_001269800.1:p.Ser248=
  • NP_001269800.1:p.Ser248Arg
  • NP_001269801.1:p.Ser248=
  • NP_001269801.1:p.Ser248Arg
  • NP_057208.2:p.Ser248=
  • NP_057208.2:p.Ser248Arg
  • NR_135787.1:n.1215+35411G>A
  • NR_135787.1:n.1215+35411G>T
  • NR_135788.1:n.277+36349G>A
  • NR_135788.1:n.277+36349G>T
  • NR_135789.1:n.1215+35411G>A
  • NR_135789.1:n.1215+35411G>T
  • XP_005246016.1:p.Ser248=
  • XP_005246017.1:p.Ser248=
  • XP_005246018.1:p.Ser248=
  • XP_005246019.1:p.Ser248=
  • XP_005246020.1:p.Ser248=
  • XP_016857504.1:p.Ser248=
  • XP_016857504.1:p.Ser248Arg
  • XR_946736.1:n.899C>A
  • XR_946736.1:n.899C>T
  • XR_946737.1:n.899C>A
  • XR_946737.1:n.899C>T
Links
SNP Details are organized in the following sections:
GeneView Map Submission Fasta Resource Diversity Validation

  Integrated Maps (Hint: click on 'Chr Pos' to see variant in the new NCBI variation viewer) back to top

  GeneView back to top

GeneView via direct blast against RefSeq sequences (used when no gene model is available): N/A


  Submitter records for this RefSNP Cluster back to top
The submission ss341945926 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs1053362 during BLAST analysis for the current build.


NCBI
Assay ID
Handle|Submitter IDValidation
Status
ss to rs
Orientation
/Strand
Alleles5' Near Seq 30 bp3' Near Seq 30 bpEntry
Date
Update
Date
Build
Added
Molecule
Type
Freq
Warning
Ancestral
Allele
Success
Rate
ss4419886LEE|e534402fwd/BC/Tgttcaacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcatccttg04/26/0210/10/03108cDNAunknown
ss24817617SEQUENOM|sqnm216614byFreqfwd/BC/Tgttcaacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcatccttg06/18/0408/05/04123cDNAunknown
ss3284846351000GENOMES|20100804_snps_128171_chr1_25628120fwd/C/Tgttcaacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcatccttg03/22/1103/22/11134Genomicunknown
ss341945926NHLBI-ESP|ESP2500-chr1-25628120byFreqfwd/BC/Tgttcaacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcatccttg03/25/1109/05/14134Genomicunknown
ss4897292261000GENOMES|20110521_exome_298643_chr1_25628120fwd/BC/Tgttcaacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcatccttg02/10/1202/21/12137Genomicunknown
ss1067418347JMKIDD_LAB|HGDP_exomes_chr1_25628120fwd/BC/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat07/09/1407/09/14142Genomicunknown
ss12900894161000GENOMES|PHASE3_V1_783751fwd/C/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat08/16/1408/16/14142Genomicunknown
ss1685398841EVA_EXAC|EVA_EXAC_194664fwd/C/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat03/04/1503/04/15144Genomicunknown
ss1710896033EVA_MGP|EVA_XIMO_12785fwd/BC/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat03/09/1503/09/15144Genomicunknown
ss1918172161WEILL_CORNELL_DGM|SNV:chr1:25628120fwd/BC/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat10/16/1510/16/15147Genomicunknown
ss2697509809GRF|rs1053362fwd/C/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat02/13/1702/13/17151Genomicunknown
ss2731264845GNOMAD|exomes_rs1053362fwd/C/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat05/17/1705/17/17151Genomicunknown
ss2746262134GNOMAD|coding_rs1053362fwd/C/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat05/17/1705/17/17151Genomicunknown
ss2752823012GNOMAD|rs1053362fwd/C/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat05/17/1705/17/17151Genomicunknown
ss3071294155TOPMED|TOPMed_freeze_5?chr1:25,301,629-01fwd/A/Cacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat09/28/1709/28/17151Genomicunknown
ss3071294156TOPMED|TOPMed_freeze_5?chr1:25,301,629-02fwd/C/Tacacctactatgctgtagcagtcaggtggtgacagccatctcagggtcat09/28/1709/28/17151Genomicunknown

  Fasta sequence   (Legend) back to top
>gnl|dbSNP|rs1053362|allelePos=251|totalLen=501|taxid=9606|snpclass=1|alleles='A/C/T'|mol=Genomic|build=151
 GGGGAGACGT GACTTCCCCA TCTAACTCTA AGTGACAAGG CTGAGACTCT CCAGCCCTAG
 GATTCTCATC CAAAACCCCT CGAGGCTCAG ACCTTTGGAG CAGGAGTGTG ATTCTGGCCA
 ACCACCCTCT CTGGCCCCCA GGCGCCCTCT TCTTGTGGAT GTTCTGGCCA AGTTTCAACT
 CTGCTCTGCT GAGAAGTCCA ATCGAAAGGA AGAATGCCGT GTTCAACACC TACTATGCTG
 TAGCAGTCAG
 H
 GTGGTGACAG CCATCTCAGG GTCATCCTTG GCTCACCCCC AAGGGAAGAT CAGCAAGGTG
 AGCAGGGCGC TGCCCTTGGG CAGCACTTGG GTCTAACAGG ACTAGCACAC ATATTTATGC
 CCCTCCCCAC CCCAGGGCCA GCGTGGGTTG GGAGAGGGCA TGCCGGGTGG TGGAGCTGTG
 CCTGCCTCTA CAGTGGAGCT CTAGGTAGAA TGCTGGGTGG TCACAGTGGG CCTGGGACTC
 AGGAGACTGT

  NCBI Resource Links back to top
Submitter-Referenced
dbSTSGenBank
sqnm216614 X63094 Hs.108380
dbSNP Blast Analysis
UniGene Cluster ID
269364
3D structure mapping
NP_001121163  NP_057208  

  Population Diversity (Alleles in RefSNP orientation) . See additional population frequency from 1000Genome [here] back to top

Sample AscertainmentGenotype DetailAlleles
ss#PopulationIndividual
Group
Chrom.
Sample Cnt.
SourceC/C
C/T
T/T
HWPC
T
ss1290089416EAS 1008AF 0.999000010.00100000
EUR 1006AF 1.00000000
AFR 1322AF 0.987899960.01210000
AMR 694AF 0.998599950.00140000
SAS 978AF 1.00000000
ss1685398841ExAc_Aggregated_Populations113160AF 0.998860000.00113998
ss24817617CEPH 184AF 0.969999970.03000000
ENSEMBL_Watson 2IG1.00000000 1.00000000
ENSEMBL_Venter 2IG1.00000000 1.00000000
ss341945926ESP_Cohort_Populations 4034GF0.993554770.005949430.000495790.001000000.996529520.00347050

SummaryAverage
Het.+/- std err:
Individual
Count
Founders
Count
Individual
Overlap
Genotype
Conflict
0.002+/-0.0340000

  Validation Summary: back to top
Validation statusMarker displays
Mendelian segregation
PCR results confirmed
in multiple reactions
Homozygotes detected
in individual genotype data
byClusterbyFreqWith1000GenomeDataUNKNOWNUNKNOWNUNKNOWN

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